Soil bacteria metabolize dialkylglycines such as 2-methylalanine via oxidative decarboxylation catalyzed by the vitamin B-6-dependent dialkylglycine decarboxylase (Aaslestad et al., 1984; Bailey et al., 1967; Lamartiniere et al., 1971; Sato et al., 1978).
The 2,2-dialkylglycine decarboxylase of the soil bacterium Pseudomonas cepacia was first reported by Aaslestad and Larson (1964) and was later investigated in several laboratories (Bailey and Dempsey, 1967; Bailey et al., 1970; Lamartiniere et al., 1971; Honma et al., 1972; Sato et al., 1978; and Keller and O'Leary, 1979). This pyridoxal 5'-phosphate-dependent enzyme catalyzes decomposition of substrate amino acids such as 2-methylalanine and isovaline in two steps: (i) release of carbon dioxide and ketone with transfer of the amino group to the cofactor to give enzyme-bound pyridoxamine 5'-phosphate and (ii) amino transfer from cofactor to pyruvate forming L-alanine and regenerating the cofactor in the aldehyde oxidation state. The decarboxylation step is analogous to the so-called abortive decarboxylation catalyzed by several pyridoxal 5'-phosphate-dependent amino acid decarboxylases, which competes with the normal hydrogen for carboxylate replacement reaction (Sukhareva, 1986). The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. Therefore, the question arises whether this enzyme is an aminotransferase that through evolution has added a decarboxylase capability or is a decarboxylase that has evolved an amino transfer capability. I provide a preliminary answer to this question by showing that the dialkylglycine decarboxylase primary structure is homologous to several aminotransferases but not to decarboxylases.
While the dialkylglycines, 2-methylalanine and isovaline (2-ethylalanine), which are substrates for the enzyme and induce dgdA gene expression, are present in low concentrations in soils, dialkylglycine decomposition is the most likely function of these genes. However, only the dialkylglycines, but no other small- and medium-sized protein-derived amino acids, induce dgdA gene expression. Dialkylglycines may have been introduced into soils by carbonaceous meteorites (Engel et al., 1990) or, at the Cretaceous-Tertiary boundary, by asteroid impact (Zhao et al., 1989). Another source of these amino acids may be soil fungi, such as Trichodema reesii, which produce peptide antibiotics, such as alamethicin, that contain 2-methylalanine and isovaline (Bruckner et al., 1984). Whatever the source, the dialkylglycines are rare in the soil environment. Consequently, tight control over biosynthesis of the decarboxylase appears necessary.
The biological role of the dialkylglycine decarboxylase remains unclear. The substrates 2-methylalanine and isovaline occur naturally as major constituents of cytotoxic peptides produced by soil fungi such as Trichoderma viride (Bruckner et al., 1980; Bruckner and Pryzbylaki, 1984; Schmitt and Jung, 1985) and as organic components of carbonaceous meteorites (Kvenvolden et al., 1971). Racemic isovaline and 2-methylalanine have been found recently in an iridium-rich Cretaceous-Tertiary boundary layer, further supporting an extraterrestrial source for this material (Zhao and Bada, 1989). Thus, the enzyme may have evolved to use the rare dialkylglycines of cosmic origin, or it may be a part of a metabolic pathway for breaking down cytotoxic peptides and the constituent amino acids.
The available structural information about the 2,2-dialkylglycine decarboxylase is sparse. Lamartiniere et al. (1971) showed by equilibrium sedimentation that a dialkylglycine decarboxylase isolated from P. cepacia has a molecular mass of 188 kDa with four identical 47 kDa subunits. They also reported a peptide map and amino acid composition data consistent with a 47 kDa subunit. Sato et al, (1978) also studied the P. cepacia dialkylglycine decarboxylase, showing by gel electrophoresis that the 180 kDa holoenzyme contained four identical subunits of approximately 45 kDa and presenting chemical labeling evidence for a catalytically important histidine residue.
Biochemical interest in 2-methylalanine- and isovaline-binding proteins is based in part on the ability of these proteins to discriminate between the stereoisomers of amino acids with small alpha-alkyl substituents such as alanine, isovaline, and 2-methylnorvaline. The amino acid binding sites of the dialkylglycine decarboxylase and the decarboxylase gene repressor may have some common structural features, since they both bind 2-methylalanine and related amino acids. Another enzyme, hog kidney aminoacylase, which hydrolyzes N-acyl-2,2-dialkylglycines with greater than 99% enantioselectivity (Baker et al., 1952; Keller et al., 1986; Jones et al., 1991), may have evolved similar structural features.